Ontology Service Integration by Tanmay2028 · Pull Request #680 · FAIRmat-NFDI/pynxtools

Tanmay2028 · 2025-07-30T16:33:18Z

This PR introduces a FastAPI-based ontology service for the NOMAD platform, enabling dynamic access to NeXus ontology superclasses via HTTP endpoints. The service also ensures the ontology file is always up-to-date with the latest commit from the NeXus definitions submodule and provides reasoning capabilities using Owlready2.

Key Features

Ontology File Management:
On startup, the service checks for the existence of the ontology OWL file corresponding to the latest commit hash. If missing, it regenerates the OWL file and updates the reference.
Reasoning and Inference:
The ontology is loaded and inferred using Owlready2’s reasoner. Inferred ontologies are cached in a temporary directory for efficient access.
API Endpoints: /superclasses/{class_name}: Returns the list of superclasses for a given ontology class.
Integration with pynxtools schema:
The pynxtools schema fetches superclasses and populates metadata fields accordingly.

.gitignore

src/pynxtools/nomad/ontology_service.py

src/pynxtools/nomad/schema.py

src/pynxtools/nomad/__init__.py

lukaspie · 2025-08-01T08:58:04Z

Would probably also be good to add some tests for this service

mkuehbach · 2025-08-06T16:34:08Z

Good to see these efforts from OSCARS bear fruit. Before this is gets merged the following needs to happen:

Tests as mentioned by Lukas (negotiate this as fits within OSCARS)
An update of the documentation (e.g., in the learning section, diataxis) that briefly explains the service and how it affects the UI experience when pynxtools is used in NOMAD is required
It would be ideal if the NeXusOntology repo's size gets reduced specifically when the plan is to have it as another default submodule with pynxtools.
Versioning of the NeXusOntology and the NeXus definitions is something that needs to be discussed to have a clear strategy if these should be in sync or not. Ideal would be if there is a PID-resolvable version of the NeXusOntology that we hook into at least for releases, for development purposes I agree that could be overkill.

Having the last two bullet points fixed to enable a merge or not is negotiatable, the other bullet points need to be fixed for this to become merged.

mkuehbach

see #680 (comment)

Tanmay2028 · 2025-08-11T13:13:26Z

Good to see these efforts from OSCARS bear fruit. Before this is gets merged the following needs to happen:

Tests as mentioned by Lukas (negotiate this as fits within OSCARS)

An update of the documentation (e.g., in the learning section, diataxis) that briefly explains the service and how it affects the UI experience when pynxtools is used in NOMAD is required

It would be ideal if the NeXusOntology repo's size gets reduced specifically when the plan is to have it as another default submodule with pynxtools.

Versioning of the NeXusOntology and the NeXus definitions is something that needs to be discussed to have a clear strategy if these should be in sync or not. Ideal would be if there is a PID-resolvable version of the NeXusOntology that we hook into at least for releases, for development purposes I agree that could be overkill.

Having the last two bullet points fixed to enable a merge or not is negotiatable, the other bullet points need to be fixed for this to become merged.

@mkuehbach Thank you for the comments. I will proceed working on the first two points. I am not sure what can be done to reduce the size of NeXusOntology repo. @sanbrock Do you have some suggestions here?

pyproject.toml

lukaspie

Reviewing just the docs for now. Please run mkdocs serve to check that they display fine.

Please also remove the package-lock.json